Cyclone is able to generate different kinds of graphs (metabolic, regulation) and to export them to Jung or Cytoscape for manipulation or visualisation. This page will explain how to Cyclone deals with networks.

Cyclone can be used to visualize graphs extracted from Cyclone data. Cyclone exports '.sif' files
that can be read by Cytoscape.
Below are some examples of screenshots of EcoCyc regulatory, proteic and metabolic graphs extracted from Cyclone data and displayed by Cytoscape.

This first example shows the transcriptional regulation interaction graph.

The resulting Cytoscape layout of the transcriptional regulatory network extracted from EcoCyc is shown below.Activations are representing by green edges, inhibitions are representing by blue edges. Genes are represented by square. An arrow starting from a gene indicates that the gene product is a transcription factor, acting on the targeted genes.

Below is a zoom on the transcriptional regulatory network extracted from EcoCyc.

The output graphs visualized in Cytoscape are shown below.
This is the metabolite regulatory network extracted from EcoCyc representing by the
'spring' graph layout algorithm of Cytoscape. Metabolite can act as regulators of enzymatic activity.Metabolite and reaction are representing by node. An arrow starting from a metabolite node indicates that this metabolite regulates the targeted enzymatic reaction node by inhibition or activation.

This is a zoom on the regulated metabolic network extracted from EcoCyc.